- modeller_usage - salilab.org

Problem including substrate and heme
by Jeffrey P. Jones 03 Feb '98

03 Feb '98

I am wondering what the format is for input in the alignment file of two molecules say heme (h) and myristic acid (5) distinct from the protein of interest. My guess is: AATLCLL(protein sequence)GT/h/5* The order they appear in the pdb file is AA/heme/myristate. Is this the format? When I use it the myristic acid input is ignored. Jeff -- Jeffrey P. Jones, Ph.D. Associate Professor of Pharmacology, Physiology Biochemistry and Biophysics (716)275-5371, http://cyp.medicine.rochester.edu/~jpj/jones_group.html jpj(a)cyp.medicine.rochester.edu

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Modeller 4 help!
by Nick Glover 02 Feb '98

02 Feb '98

Modeller users: As a neophyte, both to homology modeling and to the program Modeller-4, I am somewhat confused by the protocol to follow in order to generate a model of my target enzyme. I would be very grateful if the Modeller user community could help get me going! I have the sequence of my target, and five .pdb files of enzymes that belong to the same family, and share between 30 - 50% sequence similarity to the target. I want to get a 'good' model of the target - CPU time is not a problem, I would prefer to be thorough and get better results. Can anybody suggest the procedure I should follow, from the beginning! What file do I begin with? Do I write this myself? What is it called? How do I obtain an alignment file? MALIGN-3D? then CHECK_ALIGNMENT? Which script files should I run? mod model-default? How do I account for the error noted in the newsgroup archives? Any suggestions appreciated! Similarly, if anyone has modified the basic script files to good effect, I would appreciate a copy! Thanks in advance, Nick ---------- Nick Glover Department of Chemistry Simon Fraser University 8888 University Drive Burnaby, BC V5A 1S6 Canada

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O2 IRIX 6.3
by sali＠piano 28 Jan '98

28 Jan '98

The mod_iris4d executable works on our O2 IRIX 6.3. Andrej -- -- Andrej Sali, Assistant Professor The Rockefeller University, 1230 York Avenue, New York, NY 10021-6399 tel +1 212 327 7550; lab +1 212 327 7206 ; fax +1 212 327 7540 e-mail sali(a)rockvax.rockefeller.edu; http://salilab.org

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Re: Hydrogen problems with Modeller4
by Andrew Martin 26 Jan '98

26 Jan '98

> Dear Andrew and Brian! > > please replace BUILD_MODEL INITIALIZE_XYZ = off > to BUILD_MODEL INITIALIZE_XYZ = off, BUILD_METHOD = > 'INTERNAL_COORDINATES' > > in file $MODINSTALL/scripts/__generate_model.top ^^^^^^^ bin - not scripts > > and > SET TOPLIB = '${LIB}/top_allh.lib' > in your .top file. > > Happy landings! > > Yours, > > Azat > Excellent! That's certainly fixed it... But wouldn't this have been a problem affecting everybody using Modeller for straightforward homology modelling??? I haven't used the SET TOPLIB as I was not reading hydrogens, so it is taking the default SET TOPLIB = '${LIB}/top_heav.lib' I was seeing the problem with this. As far as I can see it's not really related to the hydrogens issue. My .top file was quite simply: INCLUDE SET ATOM_FILES_DIRECTORY = './:/data/pdb/' SET PDB_EXT = '.pdb' SET STARTING_MODEL = 1 SET ENDING_MODEL = 1 SET DEVIATION = 0 SET KNOWNS = 'xyz' SET HETATM_IO = off SET WATER_IO = off SET HYDROGEN_IO = off SET MD_LEVEL = 'refine1' SET ALIGNMENT_FORMAT = 'PIR' SET SEQUENCE = 'abc' SET ALNFILE = 'align.pir' CALL ROUTINE = 'model' Any thoughts??? Andrew ---------------------------------------------------------------------------- Dr. Andrew C.R. Martin University College London EMAIL: (Work) martin(a)biochem.ucl.ac.uk (Home) andrew(a)stagleys.demon.co.uk URL: http://www.biochem.ucl.ac.uk/~martin Tel: (Work) +44(0)171 419 3890 (Home) +44(0)1372 275775

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Re: Hydrogen problems with Modeller4
by Andrew Martin 23 Jan '98

23 Jan '98

I have had very similar problems with Modeller4: huge numbers of violations and gaps in the backbone even without hydrogens. However, my .top files (generated by my MINT program) contain the command SET HYDROGEN_IO=off I haven't had time to analyse exactly what's going on yet (for the moment I've gone back to Modeller3). I'll try to take another look in the next few days. I too have assumed I've been doing something stupid and have just downloaded Modeller4 again to try installing from scratch again. Andrew > What you did should work. Can you please email the input files to > azat(a)salilab.org, so that Azat can take a closer look. > > Thanks, Andrej > > > Brian Marsden wrote: > > > > I'm having a bit of a torrid time trying to get Modeller4 to cope with > > hydrogens. Here's the scenario: > > > > I have a template pdb file (directly from the Brookhaven PDB databank) > > which contains an NMR structure and therefore contains all hydrogens. > > Looking at the FAQ in Modeller's documentation I find that I probably > > need to add the following lines to get-model.top: > > > > SET HYDROGEN_IO=on > > SET TOPOLOGY_MODEL=1 > > SET TOPLIB = '${LIB}/top.lib' > > SET PARLIB = '${LIB}/par.lib' > > > > I then run Modeller in the usual way and end up with models with a huge > > number of violations, and whopping great big gaps in the backbone. > > ---------------------------------------------------------------------------- Dr. Andrew C.R. Martin University College London EMAIL: (Work) martin(a)biochem.ucl.ac.uk (Home) andrew(a)stagleys.demon.co.uk URL: http://www.biochem.ucl.ac.uk/~martin Tel: (Work) +44(0)171 419 3890 (Home) +44(0)1372 275775

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Hydrogen problems with Modeller4
by Brian Marsden 21 Jan '98

21 Jan '98

I'm having a bit of a torrid time trying to get Modeller4 to cope with hydrogens. Here's the scenario: I have a template pdb file (directly from the Brookhaven PDB databank) which contains an NMR structure and therefore contains all hydrogens. Looking at the FAQ in Modeller's documentation I find that I probably need to add the following lines to get-model.top: SET HYDROGEN_IO=on SET TOPOLOGY_MODEL=1 SET TOPLIB = '${LIB}/top.lib' SET PARLIB = '${LIB}/par.lib' I then run Modeller in the usual way and end up with models with a huge number of violations, and whopping great big gaps in the backbone. Strangely, if I strip the pdb file of all its hydrogens, remove the SET HYDROGEN_IO=on and put TOPOLOGY_MODEL to 3 everything is fine - a nice model is made, but, of course, without any hydrogens. I'm probably doing something daft - can anyone out there point me in the direction? Many thanks. Brian. --------------------------------------------------------------------- Brian Marsden marsden(a)bioch.ox.ac.uk Home: +44 1865 552696 OCMS, Oxford Fax: +44 1865 275253 Work: +44 1865 275720 ---------------------------------------------------------------------

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[Fwd: [Fwd: Segmentation Fault : Core Dumped]]
by Azat Badretdinov 21 Jan '98

21 Jan '98

-- - Dr. Azat Badretdinov - The Rockefeller Univ, Box 270 - 1230 York Ave, New York NY 10021, USA - Phone: (212) 327 7206 - Fax: (212) 327 7540 - E-mail: azat(a)salilab.org - WWW/URL: http://salilab.org/~azat

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[Fwd: [Fwd: Segmentation Fault : Core Dumped]]
by Azat Badretdinov 21 Jan '98

21 Jan '98

-- - Dr. Azat Badretdinov - The Rockefeller Univ, Box 270 - 1230 York Ave, New York NY 10021, USA - Phone: (212) 327 7206 - Fax: (212) 327 7540 - E-mail: azat(a)salilab.org - WWW/URL: http://salilab.org/~azat

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[Fwd: Segmentation Fault : Core Dumped]
by Azat Badretdinov 21 Jan '98

21 Jan '98

-- - Dr. Azat Badretdinov - The Rockefeller Univ, Box 270 - 1230 York Ave, New York NY 10021, USA - Phone: (212) 327 7206 - Fax: (212) 327 7540 - E-mail: azat(a)salilab.org - WWW/URL: http://salilab.org/~azat

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Libraries needed for MODELLER on SUN
by sali＠piano 21 Jan '98

21 Jan '98

Forwarded message:

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